Inaccuracies and simplifications are inevitable in the human perception of the phenomena of the real world, which in scientific psychology are considered as cognitive distortions. In this article, the distortions of the perception of complex multi-element systems are investigated using well-known examples of the construction and research of enterprise models in the economy. An approach is proposed to identify and analyze varieties of cognitive distortions that differ in the degree of simplification and different points of view on significant and insignificant processes and factors. The revealed varieties are called stages of cognitive distortions and are justified by the analysis of enterprise modeling. The advantages and disadvantages inherent in the stages of cognitive distortions are formulated, and the applicability of the approach to complex systems of various nature is noted.